YY1 gene transcriptions

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Associate Editor(s)-in-Chief: Henry A. Hoff

"To further explore how [high-glucose] HG regulates Tug1 transcription, we retrieved the promoter region of the murine Tug1 gene to identify potential binding sites for transcription factors. Alignment of mouse, human, and rat Tug1 promoter sequences indicated that these sequences are highly conserved, with over 90% of the sequences identical among these three species [...]. Using a web-based tool, rVista 2.0, we identified several potential binding sites for transcription factors [...]. Notably, we found multiple p53 candidate binding sites as well as SP1, YY1, E47, IRF-3, and PPAR-a binding sites."[1]

Human genes

Main article: Human genes

"The human lncRNA TUG1 gene (NCBI reference sequence NR_110492 transcript variant 1) is located on chromosome 22q12.2 and has 8 variant transcripts, ranging from 5.2–7.6 kilobase in length, whereas the murine Tug1 lncRNA locus is located on chromosome 11 and has three variant (a, b, and c) transcripts that are 4.1–6.7 kilobases long [...]."[1]

Gene expressions

Main article: Gene expressions

Transcription "factor p53 significantly activates, whereas YY1 represses, Tug1 transcription [...], consistent with the presence of consensus binding sites for these transcription factors in the promoter region (Fig. 2B) and previous reports about the induction of Tug1 expression by p53 (32, 33)."[1]

Interactions

Main article: Interaction gene transcriptions

Consensus sequences

Human, rat and murine have the YY1 consensus sequences CCATTTA and CCATCTT.[1]

Binding site for

Enhancer activity

Main article: Enhancer activity copy gene transcriptions

Promoter occurrences

Main article: Promoter occurrence gene transcriptions

Hypotheses

Main article: Hypotheses
  1. A1BG has no regulatory elements in either promoter.
  2. A1BG is not transcribed by a regulatory element.
  3. No regulatory element participates in the transcription of A1BG.

YY1 CCATTTA samplings

Main article: Model samplings

Copying a responsive elements consensus sequence CCATTTA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CCATTTA (starting with SuccessablesYY1.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for CCATTTA, 0.
  2. positive strand, negative direction, looking for CCATTTA, 0.
  3. positive strand, positive direction, looking for CCATTTA, 0.
  4. negative strand, positive direction, looking for CCATTTA, 0.
  5. complement, negative strand, negative direction, looking for GGTAAAT, 0.
  6. complement, positive strand, negative direction, looking for GGTAAAT, 0.
  7. complement, positive strand, positive direction, looking for GGTAAAT, 0.
  8. complement, negative strand, positive direction, looking for GGTAAAT, 0.
  9. inverse complement, negative strand, negative direction, looking for TAAATGG, 0.
  10. inverse complement, positive strand, negative direction, looking for TAAATGG, 0.
  11. inverse complement, positive strand, positive direction, looking for TAAATGG, 0.
  12. inverse complement, negative strand, positive direction, looking for TAAATGG, 0.
  13. inverse negative strand, negative direction, looking for ATTTACC, 0.
  14. inverse positive strand, negative direction, looking for ATTTACC, 0.
  15. inverse positive strand, positive direction, looking for ATTTACC, 0.
  16. inverse negative strand, positive direction, looking for ATTTACC, 0.

YY1 CCATCTT samplings

Copying a responsive elements consensus sequence CCATCTT and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or one between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CCATCTT (starting with SuccessablesYY1.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for CCATCTT, 1, CCATCTT at 1654.
  2. positive strand, negative direction, looking for CCATCTT, 0.
  3. positive strand, positive direction, looking for CCATCTT, 0.
  4. negative strand, positive direction, looking for CCATCTT, 0.
  5. complement, negative strand, negative direction, looking for GGTAGAA, 0.
  6. complement, positive strand, negative direction, looking for GGTAGAA, 1, GGTAGAA at 1654.
  7. complement, positive strand, positive direction, looking for GGTAGAA, 0.
  8. complement, negative strand, positive direction, looking for GGTAGAA, 0.
  9. inverse complement, negative strand, negative direction, looking for AAGATGG, 0.
  10. inverse complement, positive strand, negative direction, looking for AAGATGG, 0.
  11. inverse complement, positive strand, positive direction, looking for AAGATGG, 0.
  12. inverse complement, negative strand, positive direction, looking for AAGATGG, 0.
  13. inverse negative strand, negative direction, looking for TTCTACC, 0.
  14. inverse positive strand, negative direction, looking for TTCTACC, 0.
  15. inverse positive strand, positive direction, looking for TTCTACC, 0.
  16. inverse negative strand, positive direction, looking for TTCTACC, 0.

YY1CTT negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: CCATCTT at 1654.

YY1T random dataset samplings

  1. YY1Tr0: 0.
  2. YY1Tr1: 0.
  3. YY1Tr2: 1, CCATCTT at 210.
  4. YY1Tr3: 0.
  5. YY1Tr4: 0.
  6. YY1Tr5: 0.
  7. YY1Tr6: 0.
  8. YY1Tr7: 0.
  9. YY1Tr8: 1, CCATCTT at 1395.
  10. YY1Tr9: 1, CCATCTT at 3409.
  11. YY1Tr0ci: 0.
  12. YY1Tr1ci: 0.
  13. YY1Tr2ci: 0.
  14. YY1Tr3ci: 1, AAGATGG at 4409.
  15. YY1Tr4ci: 2, AAGATGG at 3743, AAGATGG at 3202.
  16. YY1Tr5ci: 1, AAGATGG at 1038.
  17. YY1Tr6ci: 0.
  18. YY1Tr7ci: 0.
  19. YY1Tr8ci: 0.
  20. YY1Tr9ci: 0.

YY1Tr arbitrary (evens) (4560-2846) UTRs

  1. YY1Tr4ci: AAGATGG at 3743, AAGATGG at 3202.

YY1Tr alternate (odds) (4560-2846) UTRs

  1. YY1Tr9: CCATCTT at 3409.
  2. YY1Tr3ci: AAGATGG at 4409.

YY1Tr arbitrary positive direction (odds) (4445-4265) core promoters

  1. YY1Tr3ci: AAGATGG at 4409.

YY1Tr arbitrary negative direction (evens) (2596-1) distal promoters

  1. YY1Tr2: CCATCTT at 210.
  2. YY1Tr8: CCATCTT at 1395.

YY1Tr alternate negative direction (odds) (2596-1) distal promoters

  1. YY1Tr5ci: AAGATGG at 1038.

YY1Tr arbitrary positive direction (odds) (4050-1) distal promoters

  1. YY1Tr9: CCATCTT at 3409.
  2. YY1Tr5ci: AAGATGG at 1038.

YY1Tr alternate positive direction (evens) (4050-1) distal promoters

  1. YY1Tr2: CCATCTT at 210.
  2. YY1Tr8: CCATCTT at 1395.
  3. YY1Tr4ci: AAGATGG at 3743, AAGATGG at 3202.

YY1CTT analysis and results

Main article: Complex locus A1BG and ZNF497 § YY1Ts

Human, rat and murine have the YY1 consensus sequences CCATTTA and CCATCTT.[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 1 10 0.1 0.15
Randoms UTR alternate negative 2 10 0.2 0.15
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 1 10 0.1 0.05
Randoms Core alternate positive 0 10 0 0.05
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 1 2 0.5 0.5 ± 0.5 (--1+-0)
Randoms Distal arbitrary negative 2 10 0.2 0.15
Randoms Distal alternate negative 1 10 0.1 0.15
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 2 10 0.2 0.3
Randoms Distal alternate positive 4 10 0.4 0.3

Comparison:

The occurrences of real YY1CTT distals are greater than the randoms. This suggests that the real YY1CTT distals are likely active or activable.

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Jianyin Long; Daniel L. Galvan; Koki Mise; Yashpal S. Kanwar; Li Li; Naravat Poungavrin; Paul A. Overbeek; Benny H. Chang; Farhad R. Danesh (28 May 2020). "Role for carbohydrate response element-binding protein (ChREBP) in high glucose-mediated repression of long noncoding RNA Tug1" (PDF). Journal of Biological Chemistry. 5 (28). doi:10.1074/jbc.RA120.013228. Retrieved 6 October 2020.

External links

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